FAIRMol

OHD_TB2022_20

Pose ID 8880 Compound 636 Pose 72

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand OHD_TB2022_20
PDB1NJJ↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
32.0 kcal/mol
Protein clashes
0
Internal clashes
14
Native overlap
contact recall 0.60, Jaccard 0.45, H-bond role recall 0.20
Burial
74%
Hydrophobic fit
84%
Reason: 14 internal clashes
14 intramolecular clashes 36% of hydrophobic surface appears solvent-exposed (8/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.727 kcal/mol/HA) ✓ Good fit quality (FQ -7.01) ✓ Good H-bonds (3 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Very high strain energy (32.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-21.798
kcal/mol
LE
-0.727
kcal/mol/HA
Fit Quality
-7.01
FQ (Leeson)
HAC
30
heavy atoms
MW
400
Da
LogP
2.26
cLogP
Strain ΔE
32.0 kcal/mol
SASA buried
74%
Lipo contact
84% BSA apolar/total
SASA unbound
677 Ų
Apolar buried
425 Ų

Interaction summary

HB 3 HY 14 PI 0 CLASH 0 ⚠ Exposure 36%
⚠️Partial hydrophobic solvent exposure
36% of hydrophobic surface appears solvent-exposed (8/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 22 Buried (contacted) 14 Exposed 8 LogP 2.26 H-bonds 3
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank2.689Score-21.798
Inter norm-0.751Intra norm0.024
Top1000noExcludedno
Contacts14H-bonds3
Artifact reasongeometry warning; 14 clashes; 1 protein clash; high strain Δ 32.0
Residues
ARG22 ARG342 ASN20 CYS26 GLN341 GLU343 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 THR21 THR285

Protein summary

398 residues
Protein targetT14Atoms6140
Residues398Chains1
Residue summaryVAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:ORX602

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap9Native recall0.60
Jaccard0.45RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
59 1.8077656603314811 -1.33737 -41.1817 8 18 0 0.00 0.00 - no Open
21 1.8167442151259838 -1.3248 -40.6867 9 18 0 0.00 0.00 - no Open
69 2.0383590711769224 -1.31566 -36.354 9 18 0 0.00 0.00 - no Open
18 2.07494107366931 -1.35194 -41.1881 8 18 0 0.00 0.00 - no Open
51 2.4756796252970026 -0.987142 -25.1715 6 16 0 0.00 0.00 - no Open
17 2.659480533179131 -0.988025 -29.206 7 15 0 0.00 0.00 - no Open
72 2.6888440031633536 -0.750575 -21.7979 3 14 9 0.60 0.20 - no Current
17 3.58601093162473 -0.977028 -29.0743 11 20 0 0.00 0.00 - no Open
44 3.8186271411229127 -0.825732 -21.4312 7 17 0 0.00 0.00 - no Open
69 3.822991328266453 -0.994304 -25.3242 10 18 0 0.00 0.00 - no Open
15 3.9945811977562276 -1.07747 -28.4735 11 20 0 0.00 0.00 - no Open
6 4.1125363457515824 -0.789709 -22.5077 7 16 0 0.00 0.00 - no Open
59 4.174917693331722 -0.958177 -28.341 9 18 0 0.00 0.00 - no Open
51 4.210198956266459 -1.07569 -27.4595 10 20 0 0.00 0.00 - no Open
18 4.247291649628563 -0.861737 -21.7221 4 20 0 0.00 0.00 - no Open
77 4.253748462384305 -0.861034 -20.9423 10 20 0 0.00 0.00 - no Open
15 4.305552679508108 -0.796609 -24.1605 4 14 0 0.00 0.00 - no Open
14 4.938291489005273 -0.642126 -17.5617 5 14 0 0.00 0.00 - no Open
67 5.1022653534044835 -0.644701 -19.1146 6 14 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -21.798kcal/mol
Ligand efficiency (LE) -0.7266kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.009
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 400.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.26
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 11.94kcal/mol
Minimised FF energy -20.01kcal/mol

SASA & burial

✓ computed
SASA (unbound) 677.0Ų
Total solvent-accessible surface area of free ligand
BSA total 503.0Ų
Buried surface area upon binding
BSA apolar 424.5Ų
Hydrophobic contacts buried
BSA polar 78.5Ų
Polar contacts buried
Fraction buried 74.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2521.0Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1385.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)